Here's why human women probably struggled to have babies with Neanderthal men

Imagine a couple living between 39,000 and 45,000 years ago. She's a human. He's a Neanderthal. Their families aren't thrilled with the union, but they've learned to deal with it.

Their union isn't all that unusual after all — enough humans and Neanderthals made babies together in the 5,000-plus years that the two species coexisted that modern humans now owe about 4% of our DNA to our extinct nonhuman kin.

As this human-Neanderthal couple moves through life, like many couples, they have children. A daughter, and then another daughter, and then another. And they notice something funny: All their Neanderthal man/human woman couple friends keep having daughters as well.

That mystery may have puzzled them, and its genetic legacy has puzzled modern scientists as well. While traces of all sorts of Neanderthal DNA show up in the human genome, scientists haven't found any Neanderthal Y-chromosomes — the chromosomes fathers pass to biologically male children. That doesn't necessarily mean the Neanderthal Y-chromosome is extinct, but it makes it likely.

There are a number of theories as to why the Neanderthal Y has vanished, the most popular until recently being the vagaries of random chance. That is, that male children were born to Neanderthal-human couples, but their genes were rare enough not to survive through the ages.

But a study published recently in the American Journal of Human Genetics suggests an alternate explanation: Human women may have been unable, or at least struggled, to carry male half-Neanderthal fetuses to term. That's because of three genes found on the Neanderthal Y-chromosome that are known to trigger immune responses in human beings. Those genes could have caused human mothers' immune systems to attack male half-Neanderthal fetuses, triggering miscarriages.

Even if half-Neanderthal baby boys with human mothers were born occasionally, that genetic incompatibility could have weeded out enough of them to eventually remove their traces from the gene pool.

The paper's authors caution that their results are not conclusive — they've identified a possible cause, not shown it to be the case. But for bemused parents at ancient play groups full of little half-Neanderthal girls (as well as modern scientists) this result might have sated some curiosity.